rs6889356

Positions:

• chr5-147894213-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206966.3(C5orf46):​c.*10-1274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,138 control chromosomes in the GnomAD database, including 4,747 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (4747 hom., cov: 31)
• Consequence: C5orf46 NM_206966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

Genes affected

C5orf46 (HGNC:33768): (chromosome 5 open reading frame 46) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf46	NM_206966.3	c.*10-1274A>G		intron_variant		ENST00000318315.5	NP_996849.2
C5orf46	XM_005268446.4	c.*9+2771A>G		intron_variant			XP_005268503.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf46	ENST00000318315.5	c.*10-1274A>G		intron_variant		1	NM_206966.3	ENSP00000315370	P1
C5orf46	ENST00000510432.1	n.204+7416A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22894 AN: 152020 Hom.: 4718 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.00963

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.00762

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152138 Hom.: 4747 Cov.: 31 AF XY: 0.147 AC XY: 10973 AN XY: 74398

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.00965

Gnomad4 SAS AF: 0.0327

Gnomad4 FIN AF: 0.00762

Gnomad4 NFE AF: 0.0237

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0524 Hom.: 863

Bravo AF: 0.169

Asia WGS AF: 0.0470 AC: 165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6889356; hg19: chr5-147273776;